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The Indian black clam  Villorita cyprinoides  (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of  Villorita . The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of  V. cyprinoides  using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to  Corbicula fluminea . The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs,  rrn S and  rrn L) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered  V. cyprinoides  and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of  V. cyprinoides  and  C. fluminea,  analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus  Villorita . Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.

Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications